Kyrgyzstan's prime minister resigned on Monday after he came under parliamentary fire during a probe targeting alleged corruption in the communications sector.

Last month Muhammedkalyi Abylgaziyev took a holiday from work as investigators probed a suspect sale of national radio frequencies involving a leading cable television company and a major telecoms company. 

While stressing his innocence and noting he has not been questioned, Abylgaziyev said in a statement that he had decided to resign due to "uncertainty (which) disturbs the full functioning of the government".

Prior to his resignation, lawmakers had raised suspicions over his involvement in the sale, even though he has not been named as a suspect by investigators.

Investigators arrested a former head of the government's communications agency and a director at a cable television company last month.

Despite lasting just over two years in his post, Abylgaziyev, 52, is the longest-serving Kyrgyz premier in the decade since a popular uprising unseated the authoritarian leader Kurmanbek Bakiyev in 2010.

He was parachuted into the role having previously served as incumbent president Sooronbay Jeenbekov's chief of staff. 

Kyrgyzstan is the least authoritarian of the five Central Asian "stans" that gained independence from the Soviet Union in 1991 but also the second poorest and the most politically volatile.